I have followed the workflow described originally in the bash script and then in the md file.
Everything seems to work until the solve step, which fails after a few seconds with this message ( i shortened it a bit, but can add the whole thing if that is interesting.)
# Finding the neutral diploid/tetraploid cluster
## Cluster selected as neutral (diploid/tetraploid) is 29
# Running diploid
## Running diploid with 2 clones
### Running command: /home/shollizeck/hatchet/lib/python2.7/site-packages/hatchet-0.1.0-py2.7-linux-x86_64.egg/hatchet/solve /home/shollizeck/test_hatchet//bbc/bulk -f -e 6 -j 2 -p 400 -u 0.03 -r 12 -M 2 -v 2 -c 29:1:1 -n 2 -o /home/shollizeck/test_hatchet//results/results.diploid.n2
## M: 2
## mR: 0.08
## mB: 0.04
## m: None
## clonal: None
## tR: 0.08
## seg: /home/shollizeck/test_hatchet//bbc/bulk.seg
## tetraploid: False
## diploid: False
## eT: 12
## r: 12
## tB: 0.04
## u: 0.03
## x: /home/shollizeck/test_hatchet//results
## f: None
## d: None
## g: 0.35
## solver: /home/shollizeck/hatchet/lib/python2.7/site-packages/hatchet-0.1.0-py2.7-linux-x86_64.egg/hatchet/solve
## ln: 2
## eD: 6
## j: 2
## bbc: /home/shollizeck/test_hatchet//bbc/bulk.bbc
## ts: 0.008
## p: 400
## s: None
## un: 8
## limit: 0.6
## v: 3
## input: /home/shollizeck/test_hatchet//bbc/bulk
## td: 0.1
## ampdel: True
## tc: 1
Traceback (most recent call last):
File "/usr/lib64/python2.7/runpy.py", line 162, in _run_module_as_main
"__main__", fname, loader, pkg_name)
File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/home/shollizeck/hatchet/lib/python2.7/site-packages/hatchet-0.1.0-py2.7-linux-x86_64.egg/hatchet/__main__.py", line 45, in <module>
solve([solve_bin] + args)
File "/home/shollizeck/hatchet/lib/python2.7/site-packages/hatchet-0.1.0-py2.7-linux-x86_64.egg/hatchet/bin/HATCHet.py", line 189, in main
diploidObjs = runningDiploid(neutral=neutral, args=args)
File "/home/shollizeck/hatchet/lib/python2.7/site-packages/hatchet-0.1.0-py2.7-linux-x86_64.egg/hatchet/bin/HATCHet.py", line 378, in runningDiploid
results.append((n , execute(args, basecmd, n, outprefix), outprefix))
File "/home/shollizeck/hatchet/lib/python2.7/site-packages/hatchet-0.1.0-py2.7-linux-x86_64.egg/hatchet/bin/HATCHet.py", line 641, in execute
raise RuntimeError(error("The following command failed: \n\t\t{}\nwith {}\n".format(cmd, buffer)))
RuntimeError: The following command failed:
/home/shollizeck/hatchet/lib/python2.7/site-packages/hatchet-0.1.0-py2.7-linux-x86_64.egg/hatchet/solve /home/shollizeck/test_hatchet//bbc/bulk -f -e 6 -j 2 -p 400 -u 0.03 -r 12 -M 2 -v 2 -c 29:1:1 -n 2 -o /home/shollizeck/test_hatchet//results/results.diploid.n2
with ['\x1b[95m\x1b[1m[21:06:31]### Parsing and checking input arguments\t\x1b[0m', '\x1b[92m[21:06:31]## \tInput prefix: /home/shollizeck/test_hatchet//bbc/bulk', 'Input SEG: /home/shollizeck/test_hatchet//bbc/bulk.seg', 'Input BBC: /home/shollizeck/test_hatchet//bbc/bulk.bbc', 'Number of clones: 2', 'Clonal copy numbers: { 29 [Cluster] : 1|1 [CN] }', 'Help message: 0', 'Maximum number of copy-number states: -1', 'Maximum integer copy number: 6', 'Number of jobs: 2', 'Number of seeds: 400', 'Minimum tumor-clone threshold: 0.03', 'Maximum resident memory: -1', 'Time limit: -1', 'Maximum number of iteratios: 10', 'Random seed: 12', 'Solving mode: Coordinate-descent only', 'Verbose: 2', 'Output prefix: /home/shollizeck/test_hatchet//results/results.diploid.n2', 'Diploid threshold: 0.1', 'Base: 1', 'Force amp-del: 1\t\x1b[0m', '\x1b[95m\x1b[1m[21:06:31]### Reading the input SEG file\t\x1b[0m', '\x1b[95m\x1b[1m[21:06:31]### Scale the read-depth ratios into fractional copy numbers using the provided copy numbers\t\x1b[0m', '\x1b[95m\x1b[1m[21:06:31]### Compute allele-specific fractional copy numbers using BAF\t\x1b[0m', '\x1b[95m\x1b[1m[21:06:31]### Starting coordinate descent algorithm on 400 seeds\t\x1b[0m', '\x1b[92m[21:06:31]## Coordinate Descence {\t\x1b[0m', "terminate called after throwing an instance of 'GRBException'", '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', 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I just dont even know where to do something different, so any help/fix would be amazing.